GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility

Predicting conformational changes of both the protein and the ligand is a major challenge when a protein–ligand complex structure is predicted from the unbound protein and ligand structures. Herein, we introduce a new protein–ligand docking program called GalaxyDock3 that considers the full ligand conformational flexibility by explicitly sampling the ligand ring conformation and allowing the relaxation of the full ligand degrees of freedom, including bond angles and lengths. This method is based on the previous version (GalaxyDock2) which performs the global optimization of a designed score function. Ligand ring conformation is sampled from a ring conformation library constructed from structure databases. The GalaxyDock3 score function was trained with an additional bonded energy term for the ligand on a large set of complex structures. The performance of GalaxyDock3 was improved compared to GalaxyDock2 when predicted ligand conformation was used as the input for docking, especially when the input ligand conformation differs significantly from the crystal conformation. GalaxyDock3 also compared favorably with other available docking programs on two benchmark tests that contained diverse ligand rings. The program is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html . © 2019 Wiley Periodicals, Inc.     

Protein–small molecule docking with receptor flexibility in iMOLSDOCK

We have earlier reported the iMOLSDOCK technique to perform ‘induced-fit’ peptide–protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein–ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time. The source code and binary of MOLS 2.0 (under a GNU Lesser General Public License) are freely available for download at https://sourceforge.net/projects/mols2-0/files/.     

Protein–ligand docking using FFT based sampling: D3R case study

Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein–peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein–ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein–ligand interaction landscape, which will be explored in further applications.     

Gel-state polybenzimidazole proton exchange membranes with flexible alkyl sulfonic acid side chains for a wider operating temperature range(25–240 ℃)

High-temperature proton exchange membrane fuel cells(HT-PEMFC) possess distinct technical advantages of high output power, simplified water/heat management, increased tolerance to fuel impurities and diverse fuel sources, within the temperature range of 120–200 ℃. However, for practical automobile applications, it was crucial to broaden their low-temperature operating window and enable cold start-up capability. Herein, gel-state phosphoric acid(PA) doped sulfonated polybenzimidazole(PBI) proton ...     

Structure-odor relationships of α-santalol derivatives with modified side chains

(Z)-α-Santalol, which has a unique woody odor, is a main constituent of sandalwood essential oil. We investigated the structure-odor relationship of (Z)-α-santalol and its derivatives, focusing on the relationship between the structure of the side chain and the odor of the compounds. Various α-santalol derivatives (aldehydes, formates, and acetates) were synthesized from (Z)- and (E)-α-santalol, which were prepared from (+)-3-bromocamphor through modifications of a reported synthetic route. The Z- and E-isomers of α-santalols have different double-bond configurations in the side chain. Analogues with saturated side chains were also prepared from the corresponding α-santalols, and the odors of the all the prepared compounds were evaluated. We found that the odors of the Z-isomers (woody) were similar to those of the corresponding saturated compounds, but clearly different from the odors of the corresponding E-isomers (odorless, fresh, or fatty). These results indicate that the relative configuration of the side chain with respect to the santalane frame plays an important role in the odor of α-santalol. E-configuration in the side chain eliminates the woody odor character of α-santalol and its examined derivatives, whereas the Z-configuration or saturation of the carbon side chain does not.     

Synthesis and photovoltaic properties of phthalocyanine end-capped copolymers with conjugated dithienylbenzothiadiazole–vinylene side chains

Two phthalocyanine end-capped copolymers with conjugated dithienylbenzothiadiazole–vinylene side chains, PHY1 and PHY2, have been synthesized according to the Stille–Coupling polymerization method. The structures, thermostability, optical and electrochemical properties of the copolymers were characterized via NMR, GPC, TGA, DSC, UV–vis, photoluminescence (PL) spectroscopy, and cyclic voltammetry (CV), respectively. The two copolymers exhibit excellent film-forming ability and good thermostability in a wide temperature range. PHY1 and PHY2 end-capped with different phthalocyanines showed broad absorption bands ranging from the ultraviolet to the red/near-infrared (IR) region of the solar spectrum and deep HOMO energy levels. Bulk heterojunction polymer solar cells were fabricated based on PHY1 and PHY2 with [6,6]-phenyl-C₆₁-butyric acid methyl ester (PC₆₁BM) as the electron acceptor and showed power conversion efficiencies (PCE) of 1.56% and 1.26%, respectively, under the illumination of AM 1.5, 100 mW/100 cm².     

An improved adaptive genetic algorithm for protein–ligand docking

A new optimization model of molecular docking is proposed, and a fast flexible docking method based on an improved adaptive genetic algorithm is developed in this paper. The algorithm takes some advanced techniques, such as multi-population genetic strategy, entropy-based searching technique with self-adaptation and the quasi-exact penalty. A new iteration scheme in conjunction with above techniques is employed to speed up the optimization process and to ensure very rapid and steady convergence. The docking accuracy and efficiency of the method are evaluated by docking results from GOLD test data set, which contains 134 protein-ligand complexes. In over 66.2% of the complexes, the docked pose was within 2.0 A root-mean-square deviation (RMSD) of the X-ray structure. Docking time is approximately in proportion to the number of the rotatable bonds of ligands.     

Enantiorecognition ability of peptoids with α-chiral, aromatic side chains

The enantiorecognition ability of oligomeric N-substituted glycines or "peptoids" with α-chiral, aromatic side chains was investigated by HPLC and (1)H NMR studies.     

Protein–ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein–ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein–ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.     

Synthesis of pH-responsive polysilane with polyelectrolyte side chains through γ-ray-induced graft polymerization

Polysilanes with polyelectrolyte side chains are synthesized by two methods utilizing γ-ray-induced grafting and the pH responsiveness for one of those polymers is revealed mainly by investigating interfacial behavior of its monolayer at the air/water interface. In the first synthetic method, poly(methyl acrylate) is grafted onto poly(methyl-n-propylsilane) (PMPrS) through γ-ray-induced grafting, and then the PMA chains are hydrolyzed to poly(acrylic acid) resulting in the yield of ca. 97%. Thus PMPrS with polyelectrolyte side chains is successfully synthesized by the graft chain hydrolysis. The other method is the direct grafting of electrolyte monomers. Poly(methacrylic acid)-grafted PMPrS (PMPrS-g-PMAA) can be obtained through γ-ray-induced grafting of methacrylic acid monomers onto PMPrS chains, which shows the effectiveness of radiation grafting for the synthesis of polyelectrolyte graft copolymers. PMPrS-g-PMAA exhibits pH responsive behavior. In addition to the pH-dependence of water solubility, interfacial behavior also depends on the pH. Langmuir monolayers of PMPrS-g-PMAA exhibit different surface pressure-area isotherms according to the grafting yield and the pH of the subphase water. This result suggests that radiation modification is useful for fabricating polysilane-based ordered materials responsive to outer stimuli.     

Synthesis and characterization of organic–inorganic macrocyclic molecular brushes with poly(ε-caprolactone) side chains

In this work, we reported the synthesis of a dodecahydroxyl-functionalized macrocyclic oligomeric silsesquioxane (MOSS). The novel 24-membered hydroxyl-functionalized MOSS was employed as a macroinitiator for the ring-opening polymerization of ε-caprolactone (CL) and the organic–inorganic macrocyclic molecular brushes with poly(ε-caprolactone) (PCL) side chains were successfully synthesized. The organic–inorganic macrocyclic molecular brushes were characterized by means of nuclear magnetic resonance spectroscopy (NMR) and gel permeation chromatography (GPC). The results of wide angle X-ray diffraction (XRD) indicate that the architecture of the organic–inorganic macrocyclic molecular brushes did not alter the structure of PCL crystals. Differential scanning calorimetry (DSC) shows that the architecture of organic–inorganic macrocyclic molecular brushes significantly affected the rearrangement of PCL crystals. Compared to linear PCL, the organic–inorganic macrocyclic molecular brushes possessed the improved thermal stability in terms of the temperatures at the maximum of degradation rate and the yields of degradation residues.     

A new POM-templated metal–organic complex based on the flexible bis-pyridyl-bis-amide ligand

A new POM-templated metal?Corganic complex [Cu₄(L)₇(H₂O)₁₂(SiMo₁₂O₄₀)₂]·7H₂O [L?=?N,N??-bis(3-pyridinecarboxamide)-1,6-hexane], has been hydrothermally synthesized and characterized by elemental analysis, IR, TG and single-crystal X-ray diffraction analysis. The results reveal that the complex is a 2D metal?Corganic coordination framework of [Cu₄(L)₇(H₂O)₁₂] _n ⁸ⁿ⁺ cations containing decanuclear cycles with dimensions of ca. 17.55?×?57.42 ?, in which the SiMo₁₂O₄₀ ^4? anions act as non-coordinated anionic templates. The electrochemical properties of a bulk-modified carbon paste electrode of the complex have been investigated, and the results indicate that the complex-modified CPE has good electrocatalytic activity toward the reduction of nitrite in aqueous 1?M H₂SO₄ solution.     

Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry

Interactions between biomolecules control the processes of life in health and their malfunction in disease, making their characterization and quantification essential. Immobilization- and label-free analytical techniques are desirable because of their simplicity and minimal invasiveness, but they struggle with quantifying tight interactions. Here, we show that mass photometry can accurately count, distinguish by molecular mass, and thereby reveal the relative abundances of different unlabelled biomolecules and their complexes in mixtures at the single-molecule level. These measurements determine binding affinities over four orders of magnitude at equilibrium for both simple and complex stoichiometries within minutes, as well as the associated kinetics. These results introduce mass photometry as a rapid, simple and label-free method for studying sub-micromolar binding affinities, with potential for extension towards a universal approach for characterizing complex biomolecular interactions.     

Recognition of G-quadruplex DNA by triangular star-shaped compounds: with or without side chains?

We report the synthesis of two new series of triangular aromatic platforms, either with three aminoalkyl side chains (triazatrinaphthylene series, TrisK: six compounds), or without side chains (triazoniatrinaphthylene, TrisQ). The quadruplex-DNA binding behavior of the two series, which differ essentially by the localization of the cationic charges, was evaluated by means of FRET-melting and G4-FID assays. For the trisubstituted triazatrinaphthylenes (TrisK), the length of the substituents and the presence of terminal hydrogen-bond-donor groups (NH(2)) were shown to be crucial for ensuring a high quadruplex affinity (ΔT(1/2) values of up to 20 °C at 1 μM for the best candidate, TrisK3-NH) and selectivity versus duplex DNA. Subsequently, comparison of data collected on both the telomeric- and c-myc-quadruplex showed that the nonsubstituted TrisQ is even more efficient than TrisK3-NH, both in terms of quadruplex affinity (ΔT(1/2)=26 °C in K(+) buffer) and selectivity versus duplex DNA. Structural considerations conducted with the c-myc quadruplex indicate that both TrisK3-NH and TrisQ stack well onto the G-quartet but in an offset position, which might be influenced by the formation of multiple hydrogen bonds with the target in the former case. Finally, the nonsubstituted TrisQ displays a binding profile very similar to some of the best quadruplex binders, BRACO-19 and bisquinolinium 360A, used herein as references, and thereby represents a highly promising novel molecular design for quadruplex recognition.     

GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

Protein–ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein–ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein–ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.     

Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.      

Thermotropic liquid-crystalline comb-like polymers with polyacrylamide main chain—I. Synthesis and mesomorphic structures of polymers with lipobiphenyl side chains

The synthesis of polymerizable lipobiphenyls, the study of the kinetics of their radical polymerization giving comb-like polymers, and the study of the thermotropic behaviour of the polymers are reported. Utilization of all the information provided by X-ray diffraction diagrams showed that polymers with polyacrylamide main chains and lipobiphenyl side chains exhibit successively, between room temperature and isotropization temperature, two mesophases: an ordered tilted double layer smectic phase SI2, and a disordered tilted double layer smectic phase SC2.     

Two new dinuclear complexes with flexible bipyrazole ligand bridged via μ-Cl or μ1,1-N3

Two dinuclear complexes, {[Cd(bdpp)Cl₂](CH₃OH)}₂ (1) and [Cd(bdpp)(N₃)(NO₃)]₂ (2), have been synthesized by reactions of bdpp with cadmium salts (bdpp?=?1,3-bis(3′,5′-dimethylpyrazol-1′-yl)propane), and characterized by IR, element analysis, fluorescence properties and single crystal structural analysis. Cd in 1 has a trigonal bipyramidal coordination geometry and two such units form a dimer through two μ-Cl bridges. Each Cd in 2 has a distorted octahedral coordination geometry and two Cd units form a dimer through μ_1,1-N₃ bridges. The emission spectra show λ_em?=?413?nm for 1 and λ_em?=?338?nm for 2.     

pK<Subscript>a</Subscript> based protonation states and microspecies for protein–ligand docking

In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein–ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein–Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.